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In the companion article (Giovannelli et al., 10.1021/acs.jctc.7b00594), we presented an alchemical approach, based on nonequilibrium molecular dynamics simulations, to compute absolute binding free energies of a generic host-guest system. Two alternative computational routes, called binded-domain and single-point alchemical-path schemes, have been proposed. This study is addressed to furnish numerical validation and illustrative examples of the above-mentioned alchemical schemes. Validation is provided by comparing binding free-energy data relative to two poses of a Zn(II)·anion complex with those recovered from an alternative approach, based on steered molecular dynamics simulations. We illustrate important technical and theoretical aspects for a good practice in applying both alchemical schemes, not only through the calculations on the Zn(II)·anion complex, but also estimating absolute binding free energies of 1:1 complexes of β-cyclodextrin with aromatic compounds (benzene and naphthalene). Comparison with experimental data and previous molecular dynamics simulation studies further confirms the validity of the present nonequilibrium-alchemical methodology.

The spectroscopic properties of As4S4 with pressure have been computed by the quantum mechanical XP-PCM method and by density functional theory periodic calculations. The comparison has allowed the interpretation of the available experimental data. By comparison of the two methods and with experiments, we show that the XP-PCM method is able to reproduce the same behavior of the periodic calculations with much lower computational cost allowing to be adopted as a first choice computational tool for a qualitative interpretation of molecular crystals properties under pressure.

Nowadays, underwater acoustic communication is an interesting topic of research. This is especially true in the case of Autonomous Underwater Vehicles (AUVs): due to the limitations of underwater environment, where wireless and radio communications are not possible, it is very important to possess efficient and reliable tools for acoustic data exchange. Indeed, an underwater network of acoustic nodes can enhance the navigation and localization capabilities of one or more vehicles. In this paper, the authors investigate the use of an AUV as a mobile bridging node within a network of fixed heterogeneous acoustic modems. In particular, MARTA AUV, developed and built by the Department of Industrial Engineering (DIEF) of the University of Florence is employed in order to enable data transmission between modems of different manufacturers. Suitable bridging tests, whose results are proposed in this paper, were executed in order to evaluate the feasibility of such approach, showing that AUVs can efficiently accomplish the role of gateway between the nodes of the network.

A correct description of electrostatic contributions in force fields for classical simulations is mandatory for an accurate modeling of molecular interactions in pure liquids or solutions. Here, we propose a new protocol for point charge fitting, aimed to take into the proper account different polarization effects due to the environment employing virtual sites and tuning the point charge within the polarizable continuum model framework. The protocol has been validated by means of molecular dynamics simulations on pure pyridine liquid and on pyridine aqueous solution, reproducing a series of experimental observables and providing the information for their correct interpretation at atomic level. A correct description of electrostatic contributions in force fields for classical simulations is mandatory for an accurate modeling of molecular interactions in pure liquids or solutions. Here, we propose a new protocol for point charge fitting, aimed to take into the proper account different polarization effects due to the environment employing virtual sites and tuning the point charge within the polarizable continuum model framework. The protocol has been validated by means of molecular dynamics simulations on pure pyridine liquid and on pyridine aqueous solution, reproducing a series of experimental observables and providing the information for their correct interpretation at atomic level.

Design of autonomous underwater vehicles is deeply influenced by required mission specifications. In particular, some activities like inspection of offshore plants or harsh marine environments require underwater vehicle with high autonomy, good propulsion performances and manoeuvrability. These features are deeply influenced by design and performances of the propulsion system. In particular, performances of underwater vehicles (both remotely operated and autonomous) are deeply influenced by four quadrants performances of propellers and by complex fluid dynamics interactions that are difficult to be, even roughly, evaluated. In this work, a study of a reconfigurable propulsion layout and its comparison with a conventional one is introduced. In particular, this study is also focused on modelling techniques that should really represent a reasonable trade-off in terms of accuracy and involved computational resources for fast prototyping and simulation of this kind of mechatronic systems.

Despite the current industrial trend towards automation, many workers are still daily exposed to heavy loads during their duties. Regarding the construction industry, the shotcrete projection results in a particularly arduous whole-body effort for the so-called “concrete reinforcement workers”. In this paper, the design of a passive robotic human assistance tool to assist workers in dealing with the specific task of shotcrete projection will be described. If the design of an effective aid plays a crucial role in improving the job’s quality, following the guidelines given by the French company Eiffage Infrastructures; besides, the acceptance of the proposed solution shall have special consideration. Therefore, starting from an in-site assessment of the scenario, the presented solution has been profoundly adjusted to address the issues coming from this particular task. The exoskeleton adaptability to different lower-limb activities has been preserved without lowering its comfort during daily life in the working area. The developed solution’s operation range has been specifically optimized to assist the worker during specific efforts without hindering the other movements.

Multiscale QM/MM approaches have become the most suitable and effective methods for the investigation of spectroscopic properties of medium- or large-size chromophores in condensed phases. On these grounds, we are developing a novel workflow aimed at improving the generality, reliability, and ease of use of the available tools. In the present paper, we report the latest developments of such an approach with specific reference to a general workplan starting with the addition of acetonitrile to the panel of solvents already available in the General Liquid Optimized Boundary (GLOB) model enforcing nonperiodic boundary conditions (NPBC). Next, the solvatochromic shifts induced by acetonitrile on both rigid (uracil and thymine) and flexible (thyrosine) chromophores have been studied introducing in our software a number of new features ranging from rigid-geometry NPBC molecular dynamics based on the quaternion formalism to a full integration of variational (ONIOM) and perturbative (perturbed matrix method (PMM)) approaches for describing different solute-solvent topologies and local fluctuations, respectively. Finally, thymine and uracil have been studied also in methanol to point out the generality of the computational strategy. While further developments are surely needed, the strengths of our integrated approach even in its present version are demonstrated by the accuracy of the results obtained by an unsupervised approach and coupled to a computational cost strongly reduced with respect to that of conventional QM/MM models without any appreciable accuracy deterioration.

We developed and validated a novel force field in the context of the AMBER parameterization for the simulation of zinc(II)-binding proteins. The proposed force field assumes nonbonded spherical interactions between the central zinc(II) and the coordinating residues. A crucial innovative aspect of our approach is to account for the polarization effects of the cation by redefining the atomic charges of the coordinating residues and an adjustment of Lennard-Jones parameters of Zn-interacting atoms to reproduce mean distance distributions. The optimal transferable parametrization was obtained by performing accurate quantum mechanical calculations on a training set of high-quality protein structures, encompassing the most common folds of zinc(II) sites. The addressed sites contain a zinc(II) ion tetra-coordinated by histidine and cysteine residues and represent about 70% of all physiologically relevant zinc(II) sites in the Protein Data Bank. Molecular dynamics simulations with explicit solvent, carried out on several zinc(II)-binding proteins not included in the training set, show that our model for zinc(II) sites preserves the tetra-coordination of the metal site with remarkable stability, yielding zinc(II)-X mean distances similar to experimental data. Finally, the model was tested by evaluating the zinc(II)-binding affinities, using the alchemical free energy perturbation approach. The calculated dissociation constants correlate satisfactorily with the experimental counterpart demonstrating the validity and transferability of the proposed parameterization for zinc(II)-binding proteins.

The paper presents the electromechanical design of an Autonomous Surface Vehicle (ASV) developed by the Department of Industrial Engineering (DIEF) of the University of Florence (UNIFI), Italy. One of the main functions of this autonomous moving buoy is to localize underwater targets, such as Autonomous Underwater Vehicles (AUVs), through an Ultra Short BaseLine (USBL) and to enable the communication with them; furthermore, it is possible to equip the buoy with sensors or payloads, for instance cameras to detect the seabed. The buoy specifications and its navigation devices are described. The main features of the developed floating device are given, starting from its system architecture to its structural design. The buoy will be assembled during Summer 2019 and tested together with the UNIFI DIEF underwater vehicles.

The structural and dynamic properties of imidazole in aqueous solution have been studied by means of classical and ab initio molecular dynamics simulations. We developed a new force field for the imidazole molecule with improved modeling of the electrostatic interactions, specifically tailored to address the well-known drawbacks of existing force fields based on the atomic fractional charge approach. To this end, we reparametrized the charge distribution on the heterocyclic ring, introducing an extra site accounting for the lone pair on the deprotonated nitrogen. The accuracy of the model in describing the hydrogen bond pattern in the aqueous solvent has been confirmed by comparing the classical results on imidazole-water interactions to accurate Car-Parrinello molecular dynamics simulations. It reproduces satisfactorily the experimental water/octanol partition coefficient of imidazole, as well as the structure of the imidazole molecular crystal. The force field has been finally applied to simulate aqueous solutions at various imidazole concentrations to obtain information on both imidazole-water and imidazole-imidazole interactions, providing a description of the different molecular arrangements in solution.

In this paper we report on the Raman scattering of antimalarial artesunate, as a neutral species and as an anion in sodium salt, and on the surface-enhanced Raman scattering (SERS) of the anion adsorbed on silver nanoparticles. The vibrational assignment of the strongest Raman peaks of artesunate has been made with reference to the Raman data on artemisinin and by identifying peaks due to modes largely localized on the succinic side chain of artesunate. The structure of artesunate, as well as that of the anion, has been optimized by means of ab-initio calculations at the DFT/B3LYP/cc-pVDZ calculation level and found in good agreement with the experimental molecular geometry. The conformational minima of the flexible side chain both in the anion and in the anion complexed with Ag+ have been characterized by ab-initio methods at the same level of accuracy and eight pairs of conformers have been predicted. From these data the vibrational frequencies and Raman intensities have been obtained. This has allowed to assign the SERS spectrum of chemisorbed artesunate to conformers with nearly all-trans side chain. For these conformers the artemisinin core lies as far as ≈ 9 A from the silver ion and the active SERS modes are localized on the succinic fragment. Minor contributions to the SERS intensity are due to the di-silver complex and a more sterically hindered mono complex. It is a major conclusion of this study that the interaction of artesunate with the silver surface is exclusively through the side chain, leaving untouched the peroxide group responsible of the antimalarial activity.

Molecular dynamics simulations have been performed to compute the solvation free energy and the octanol/water partition coefficients for a challenging set of selected organic molecules, characterized by the simultaneous presence of functional groups coarsely spanning a large portion of the chemical space in druglike compounds and, in many cases, by a complex conformational landscape (2-propoxyethanol, acetylsalicylic acid, cyclohexanamine, dialifor, ketoprofen, nitralin, profluralin, terbacil). OPLS-AA and GAFF2 parametrizations of the organic molecules and of 1-octanol have been done via the Web-based automatic parameter generators, LigParGen [ Dodda et al. Nucl. Acids Res. 2017 , 121 , 3864 ] and PrimaDORAC [ Procacci J. Chem. Inf. Model. 2017 , 57 , 1240 ], respectively. For the water solvent, three popular three-point site models, TIP3P, SPCE, and OPC3, were tested. Solvation free energies in water and 1-octanol are evaluated using a recently developed nonequilibrium alchemical technology [ Procacci et al. J. Chem. Theory Comput. 2014 , 10 , 2813 ]. Extensive and accurate simulations, including all possible combinations of organic molecule, solvent, and solvent model, are allowed to assess the accuracy with regard to solvation free energies of the latest release of two widespread force fields, OPLS and GAFF. The collected data are relevant in the evaluation of the predictive power of these classical force fields (and of the related support software for automated parametrization) with regard to binding free energies in a drug-receptor system for industrial applications.

Zeno (Zeno Environment Nautical Operator) is a compact AUV (Autonomous Underwater Vehicle) designed by the Department of Industrial Engineering of the University of Florence (UNIFI) and MDM Team S.r.l., an official spin-off company of UNIFI, within the ARCHEOSUb (Autonomous underwater Robotic and sensing systems for Cultural HEritage discovery cOnservation and in SitU valorization) European project and tailored for archaeological missions. One of the main purposes of this project is to develop low-cost AUVs, both used as a tool for services supporting the identification of new Underwater Cultural Heritage (UCH) sites and for the conservation, protection and enhancement of new and discovered ones (covering the first two phases of an archaeological campaign: search and inspection). The paper deals with the design, realization and testing of the vehicle. Its main features, payloads and implementation details are given. The official demos have already started and will be completed in autumn 2018; the different archaeological sites involved are in Italy and in Israel.

A new type of vehicle has been designed by the Department of Industrial Engineering of the University of Florence (DIEF); it is an AUV (Autonomous Underwater Vehicle) capable of switching its shape according to mission needs matching the best UUVs (Unmanned Underwater Vehicles) features: it is compact and near torpedo-shaped in case of long distance missions, such as surveillance and monitoring (closed configuration, typical of AUVs), on the other end it becomes isotropic for site inspection and on-site manipulation (open configuration, emblem of ROVs - Remotely Operated Vehicles). The main goal of the work is adding to the hydrodynamic vehicle the capability of changing its structure and its thruster configuration. The paper deals with the study and the design of the vehicle. Its main features, design choices and payloads, that can be equipped with, are described.

The problem of recovering the free energy difference between two electronic states has been investigated by Frezzato [Chem. Phys. Lett. 533, 106 (2012)], exploring the equivalence between light-absorption spectra and work distribution, hence opening to the application of a spectroscopic version of the Jarzynski equality (JE) [Phys. Rev. Lett. 78, 2690 (1997)]. Here, assuming the validity of the time-dependent perturbation theory, we demonstrate that such equivalence does not lead to the known form of the JE. This is ascribed to the fact that light-absorption processes cannot be described as stochastic processes. To emphasize such an aspect, we devise a stochastic model for the UV-vis (ultraviolet and visible) absorption, suitable for determining the free energy difference between two generic quantum manifolds in a JE-like fashion. However, the model would require explicit knowledge of the transition dipole moments, which are in general not available. Nonetheless, we derive a spectroscopic version of the JE that allows us to recover the free energy difference between the ground and an excited electronic state when the latter state is the only one observed in the spectrum.

Autonomy, performances and manoeuvrability of underwater vehicles are deeply influenced by the features of their propulsion layouts. In particular, the manoeuvrability and the reliability are very important requirements for ROV (Remotely Operated Vehicle) and AUV (Autonomous Underwater Vehicle), for this reason it is necessary to improve these features for underwater vehicles especially if they are emploied in shallow water or potentially dangerous environments. In this work are introduced an application of reconfigurable and redundant propulsion system.

The pressure-induced transformation of molecular crystals can give rise to new materials characterized by intriguing hardness or energetic properties. Mechanisms regulating these reactions at the molecular level result from a complex interplay among crystal structure, lattice dynamics, and electronic properties. Here, we show that the formation of a three-dimensional amorphous carbon nitride by compressing phase II s-triazine is controlled by the competition between two different mechanisms, one entirely structural and the other electronic, representing the first example where such occurrence is demonstrated. Temperature drives the reactivity below 8 GPa by ruling the lattice dynamics, whereas above 8 GPa the electronic modifications, uniquely governed by pressure, trigger the chemical transformation. The amorphous material synthesized has a bonding structure characterized by a bulk typical of a strongly conjugated three-dimensional carbon nitride with hydrogen atoms migrated to saturate C and N terminations.

Inspection of offshore plants or harsh marine environments, requires underwater vehicles with high autonomy, performances and maneuverability. These features are deeply affected by the design of propulsion system. An accurate design of the propulsion system, involves the modelling of the response of propellers. In this work a reconfigurable propulsion layout for an inspection vehicle is presented. Performances of the proposed solution are evaluated and compared respect to the conventional one which is currently installed on benchmark test vehicle (the MARTA AUV from University of Florence). Proposed layout exhibit superior maneuvering performances that should be useful for the inspection of offshore plants and more generally for harsh operational conditions.

The fast-switching decoupling method is a powerful nonequilibrium technique to compute absolute binding free energies of ligand-receptor complexes (Sandberg et al., J. Chem. Theory Comput. 2014, 11, 423-435). Inspired by the theory of noncovalent binding association of Gilson and co-workers (Biophys. J. 1997, 72, 1047-1069), we develop two approaches, termed binded-domain and single-point alchemical-path schemes (BiD-AP and SiP-AP), based on the possibility of performing alchemical trajectories during which the ligand is constrained to fixed positions relative to the receptor. The BiD-AP scheme exploits a recent generalization of nonequilibrium work theorems to estimate the free energy difference between the coupled and uncoupled states of the ligand-receptor complex. With respect to the fast-switching decoupling method without constraints, BiD-AP prevents the ligand from leaving the binding site, but still requires an estimate of the positional binding-site volume, which may not be a simple task. On the other side, the SiP-AP scheme allows avoidance of the calculation of the binding-site volume by introducing an additional equilibrium simulation of ligand and receptor in the bound state. In the companion article (DOI: 10.1021/acs.jctc.7b00595), we show that the extra computational effort required by SiP-AP leads to a significant improvement of accuracy in the free energy estimates.

Autonomous underwater navigation remains, as of today, a challenging task. The marine environment limits the number of sensors available for precise localization, hence Au- tonomous Underwater Vehicles (AUVs) usually rely on inertial and velocity sensors to obtain an estimate of their position either through dead reckoning or by means of more sophisticated navigation filters (such as Kalman filters and its extensions [1]). On the other hand, acoustic localization makes possible the determination of a reliable vehicles pose estimate exploiting suit- able acoustic modems [3]; such estimate can even be integrated within the navigation filter of the vehicle in order to increase its accuracy. In this paper, the authors discuss the development and the performance of an Ultra-Short BaseLine (USBL)-aided buoy to improve the localization of underwater vehicles. At first, the components and the physical realization of the buoy will be discussed; then, the procedure to compute the position of the target will be analyzed. The following part of the paper will be focused on the development of a recursive state estimation algorithm to process the measurements computed by the buoy; specifically, Extended Kalman Filter [4] has been adopted to deal with the nonlinearities of the sensors housed on the buoy. A validation of the measurement filtering through experimental tests is also proposed.

Reliable navigation systems are fundamental for Autonomous Underwater Vehicles (AUVs) to perform complex tasks and missions. It is well known that the Global Positioning System (GPS) cannot be employed in underwater scenarios; thus, during missions below the sea's surface the real-time position is usually obtained with expensive sensors, such as the Doppler Velocity Log (DVL), integrated within a navigation filter such as an Extended Kalman Filter (EKF), Unscented Kalman Filter (UKF), or Dead Reckoning (DR) strategies. The goal of this work is to develop an underwater navigation system that does not rely on a DVL and where linear speed estimations are obtained exploiting data from a Forward-Looking SONAR (FLS) or, in its absence, taking advantage of a dynamic model that presents a reduced set of parameters. The proposed solution is validated through the use of navigation data obtained during sea trials undertaken in July 2018 with FeelHippo AUV at La Spezia (Italy), at the NATO Science and Technology Organization Center for Maritime Research and Experimentation (CMRE).

The analysis of red particles in paint cross-sections from Leonardo da Vinci's Last Supper, Masolino da Panicale's wall painting Beheading of St. John the Baptist in Castiglione Olona, Tintoretto's The Discovery of the Body of Saint Mark and Paolo Veronese's Supper in the House of Simon has been carried out with micro-Raman measurements. Subtracted shifted Raman spectroscopy methods have been employed to resolve the signals in the presence of fluorescence. Taking advantage of the vibrational assignments based on recent ab initio calculations of aluminum-complexes of anthraquinones, the approach allowed the discriminate between anthraquinone dyes and lakes based on kermesic and carminic acids present in the studied samples for the first time without heavy sample treatment.

1,6-Methano[10]annulene solutions in cyclohexane have been subjected to continuous and pulsed UV irradiation. Photolysis occurs in both cases, giving naphthalene as a minor and major product, respectively. The wavelength dependence of the reaction in solution indicates that the photochemical process occurs, exciting 1,6-methano[10]annulene in the second and third singlet electronic excited states. The reaction kinetics has been determined under pulsed irradiation. From the time dependence of concentrations, along with support of density functional theory calculations and early published data, two mechanisms are proposed for naphthalene production. Reaction steps such as direct migration of the bridging methylene of 1,6-methano[10]annulene to cyclohexane and 1,6-methano[10]annulene isomerization to benzotropilidene have been identified. The calculated energy diagrams relative to the ground and lowest excited states allow one to relate these steps to processes such as electrocyclic closure and sigmatropic shift. The norcaradienic form of 1,6-methano[10]annulene results in the critical species for methylene migration and the sigmatropic [1,5] shift. The present results and those arising from photolysis in the gas phase are good examples of the photochemical reactivity of 1,6-methano[10]annulene.

Many conventional truck and working machines are equipped with additional hydraulic tooling or manipulation systems which are usually fed through a mechanical connection with the internal combustion engine, involving a poor efficiency. In particular, this is a common situation for industrial vehicles whose mission profiles involves a relevant consumption of energy by the on board hydraulic systems, respect to the one really needed for only traction purpose. In this work it is proposed an innovative solution based on the adoption of a system aimed to recover braking energy in order to feed an efficient on board hydraulic actuation system. The proposed system is then adopted to a real application, an Isuzu truck equipped with a hydraulic tooling for garbage collection. A prototype of the system has been designed, assembled and tested showing a relevant improvement of system efficiency and the feasibility of the proposed approach. In the paper the proposed solution is presented, showing the simulation models and preliminary validation results including experimental devices assembled to perform the tests.

The adsorption of isothiazole on silver colloids was studied by surface-enhanced Raman scattering (SERS) spectroscopy in comparison with other five-membered heterocycles. The experimental results coupled with those obtained by density functional theory calculations for molecule/metal complexes evidenced the presence of positively charged active sites on the surface of the silver nanoparticles, along with a close relation between ligand basicity and strong SERS effect.

The structure and the vibrational properties of the P4S3 crystal at high pressures are discussed by application of the XP-PCM method. The vibrational assignment has been clarified. The structure and the electron distribution changes as a function of pressure are analyzed. The pressure effect on the vibrational frequencies is satisfactorily reproduced and discussed in terms of confinement and structure relaxation contributions.

– The identification of adenine by surface enhanced Raman scattering (SERS) on different mineral phases of a Martian meteorite Dar al Gani (DaG) 670 has been adopted as a test to verify the capability of this technique to detect trace amounts of organic or biological substances deposited over, or contained in, extraterrestrial materials. Raman spectra of different phases of meteorite (olivine, pyroxene, and ilmenite), representative of Martian basaltic rocks, have been measured by three laser sources with wavelengths at 785, 632.8, and 514.5 nm, coupled to a confocal micro-Raman apparatus. Adenine deposited on the Martian meteorite cannot be observed in the normal Raman spectra; when, instead, meteorite is treated with silver colloidal nanoparticles, the SERS bands of adenine are strongly enhanced, allowing an easy and simple identification of this nucleobase at subpicogram level.

The hydrogen-bond dynamics of lithium nitrate trihydrate has been studied by a combined approach based on ab initio molecular dynamics simulations and wavelet analysis. The simultaneous bifurcated interaction between one hydrogen atom of water molecules and two oxygen atoms of nitrate ions is the pivotal feature of the crystal structure: this bifurcated interaction has deep effects on the O-H stretching region of the vibrational spectrum. The structural, dynamic, spectroscopic, and electronic properties of the bifurcated hydrogen bond have been investigated computationally, elucidating at the molecular level the differences with weak and strong hydrogen bonds present in the crystal. These studies corroborate the very recent IR experiments performed on the lithium nitrate trihydrate crystal, offering new perspectives to interpreting the vibrational spectra. In fact, this approach allows obtaining two-dimensional plots, which summarize the essential features of both the hydrogen-bond network and IR spectra, resulting in a peculiar "signature" of the bifurcated interaction.

Nanostructured Ag platforms have been obtained by simple chemical procedure and characterized by AFM (atomic force microscopy) measurements, for use in biosensing by means of SERS (surface-enhanced Raman scattering) spectroscopy. The SERS efficiency of these substrates has been verified by microRaman measurements on small RNA chains with different nucleobase content, showing sensitivity near attomole level. It is our opinion that these metal substrates may be widely used as appropriate sensors for detecting biomolecules in many applications concerning medical diagnostics, pharmacological research and nanomaterials technology.

The identification of two nucleobases (adenine and hypoxanthine) by Surface-Enhanced Raman Scattering (SERS) on different mineral substrates was adopted as a test case to verify the capability of this analytical technique to detect trace amounts of organic or biological substances deposited over, or contained in, Martian regolith. Raman spectra were collected on polished samples of calcite, dolomite, magnesite, siderite, anhydrite, and gypsum, onto which traces of nucleobases were added. While spectroscopic features of the two nucleobases could not be observed in normal Raman spectrum, the addition of silver nanoparticles allowed easy identification of the vibrational bands characteristic of the two nucleobases.

Four nanostructured Ag substrates have been fabricated with different surface morphologies and tested with surface-enhanced Raman scattering (SERS) experiments by adsorption of adenine. Their SERS efficiency has been compared and related to the surface roughness resulting from atomic force microscopy measurements. Chemical etching of silver by thiourea/Fe(III)nitrate produces homogeneously roughened plates, exhibiting the largest three-dimensional surface and the best SERS enhancement. They mostly exhibit surface protrusions with sizes around 200 nm, thus matching the best condition for obtaining SERS enhancement by laser excitation at 785 nm. This is quite important in the case of biomolecules, whose samples often present strong fluorescence bands, which usually are not observed with red-shifted exciting lines. Moreover, these Ag platforms, owing to their uniform nanostructured surfaces, are suitable for obtaining reproducible results from microRaman investigation. In conclusion, the present nanofabrication of Ag surfaces allows obtaining SERS-active substrates, which combine high reproducibility and sensitivity and can be successfully employed in the molecular recognition of different organic ligands or biomolecules like nucleic acids and proteins.

In order to extract spectroscopic information from trajectories obtained by classical or ab initio molecular dynamics simulations, usually Fourier transforms are employed. In recent years wavelet transforms have been shown to be a valid alternative tool to analyze time-series, due to their capability of localizing a signal both in time and frequency. In this article wavelet transforms are applied for the analysis of Car-Parrinello molecular dynamics simulations to the purpose of time-correlating structural and spectroscopic properties of methyl acetate dissolved in water and methanol. The results demonstrate the possibility of obtaining information that may be of valuable help in the interpretation of time-resolved spectroscopic data.

Ab initio molecular dynamics simulations with the Car–Parrinello method have been performed on the spodumene crystal at standard conditions and high pressure. Starting from the computed trajectories, accurate Raman and infrared spectra have been obtained and compared with available experimental measurements in the low and high pressure phases. The structural and spectroscopic changes due to the pressure effects are discussed.

Surface-enhanced Raman scattering (SERS) of adenine-containing microRNA chains has been obtained by adsorption on roughened silver substrates. The spectral features of all of these samples appear dominated by the bands of adenine. By comparison with the SERS spectra of adenine and adenosine obtained on the same substrates, along with DFT calculations on the interaction sites of adenine and adenosine with silver, inferences are discussed about the structural arrangement of the microRNA chains with respect to the metal surface. This approach gives suitable guidelines in order to investigate the adsorption of complex biomolecules on metal substrates.

SERS spectroscopy with 785-nm laser excitation minimizing fluorescence emission is exploited for remote analysis of life traces in an extraterrestrial environment. Adenine and guanine, nucleobases present in both DNA and RNA strands, and microRNA containing adenine and guanine have been used as testing ligands for identifying traces of nucleic acids in Martian rocks and sediments. SERS spectra of these nucleobase samples adsorbed on pyroxene substrates have been investigated with micro-Raman apparatus in the absence of sample manipulation and inducing the signal enhancement by deposition of silver colloidal nanoparticles over the pyroxene/nucleobase substrates. An order-of-magnitude estimate of the sample amount responsible for the SERS spectra is given. Copyright © 2009 John Wiley & Sons, Ltd.

The interactions between oxazole and water or silver nanoparticles in aqueous dispersions have been studied with a computational approach based on ab initio molecular dynamics simulations, with the Car-Parrinello method, and density functional calculations in combination with Raman and surface enhanced Raman scattering (SERS) experiments. The solvation dynamics of oxazole in water allowed for the characterization of the hydrogen bond between water and solute, which has been shown to occur essentially through the nitrogen atom of the heterocyclic molecule. To mimic the solvation process or the adsorption on silver and interpreting the corresponding Raman and SERS spectra in aqueous solution or in Ag hydrosols, density functional calculations have been carried out on model systems made up by oxazole bound to water molecules or to positively charged silver clusters. Also, the chemisorption on Ag nanoparticles is found to occur by means of the nitrogen atom of oxazole interacting with the metal substrate.

The advantages of the use of optical spectroscopy methods (infrared and Raman spectroscopy, electronic spectroscopy) in the study of high pressure transformation and chemical reactions are illustrated considering several examples. In particular, the efficiency of the spectroscopic methods in the analysis of phase transitions at high pressure, of pressure induced changes of the electronic structure and of the elucidation of the reaction mechanisms at very high pressures are considered.

The role of surface metal clusters in the surface enhanced Raman scattering (SERS) enhancement mechanism was investigated by coupling Raman measurements and DFT (density functional theory) calculations for pyrazole adsorbed on Ag colloidal nanoparticles. The adsorption process of the ligand can be suitably described by a model system constituted of pyrazolide anions chemically interacting with (Ag4)+2 surface clusters since the DFT approach allows a complete depiction of the SERS profile to be obtained, including both band frequencies and relative intensities.

Many industrial vehicles are equipped with hydraulic servo systems devoted to load manipulation and other operations that are mainly performed when the vehicle is stopped. In conventional applications hydraulic servo-system are fed by a pump directly connected to the vehicle internal engine. As a consequence the internal combustion engine cannot be switched off when the vehicle is stopped causing relevant losses and additional costs in terms of pollution, noise, fuel consumption. In this work authors propose a solution in which on board hydraulic servo system are fed using electrical energy stored in accumulators that have been previously recharged using electric regenerative braking. The proposed solution has been applied to the design of a system for a truck devoted to the collection of garbage. In the paper design criteria, simulation results and preliminary experimental data are shown in order to justify feasibility of the proposed system.

Inspection of offshore plants or harsh environments, requires underwater vehicles with high degree of autonomy, performances and maneuverability. These characteristics are deeply influenced by the features of propulsion layouts of this kind of vehicle. In particular, the study of maneuverability required by ROV and AUV implies the modelling of four quadrants operation of propellers and of three-dimensional interactions arising between complex propulsion and hull geometries. In this work, an application of reconfigurable propulsion layout of an inspection vehicle for offshore operation or harsh environments is introduced.

Clarifying the structure/dynamics relation of water hydrogen-bond network has been the aim of extensive research over many decades. By joining anvil cell high-pressure technology, femtosecond 2D infrared spectroscopy, and molecular dynamics simulations, we studied, for the first time, the spectral diffusion of the stretching frequency of an HOD impurity in liquid water as a function of pressure. Our experimental and simulation results concordantly demonstrate that the rate of spectral diffusion is almost insensitive to the applied pressure. This behavior is in contrast with the previously reported pressure-induced speed up of the orientational dynamics, which can be rationalized in terms of large angular jumps involving sudden switching between two hydrogen-bonded configurations. The different trend of the spectral diffusion can be, instead, inferred considering that the first solvation shell preserves the tetrahedral structure with pressure and the OD stretching frequency is only slight perturbed.

In this contribution we show that it is possible to build accurate force fields for small organic molecules allowing the reliable reproduction of a large panel of bulk properties, which are seldom addressed in the same context. Starting from the results obtained in recent studies, we developed a protocol for charge estimation and virtual site generation for the amide class of molecules. The parametrization of electrostatic properties is based on population analysis and orbital localization of quantum mechanical computations rooted in density functional theory and the polarizable continuum model, without any additional external information. The new protocol, coupled to other recent studies in our group targeted at an accurate fitting of internal degrees of freedom, makes available a method for building force fields from scratch (excluding for the moment intermolecular van der Waals interactions) with focus on reproducing the structure and dynamics of hydrogen bonded liquids, yielding results that are in line or better than those delivered by current general force fields. The approach is tested on the demanding series formed by formamide and its two N-methyl derivatives, N-methylformamide and N,N-dimethylformamide. We show that the atomistic structure of the liquids arising from classical molecular dynamics (MD) simulations employing the new force field is in full agreement with X-ray and neutron diffraction experiments and the corresponding spatial distribution functions are in remarkable agreement with the results of ab initio MD simulations. It is noteworthy that the latter result has never been obtained before without using ad hoc (and system dependent) scale factors and that, in addition, our parameter-free procedure is able to reproduce static dielectric constants over a wide range of values without sacrificing the force field accuracy with respect to other observables. Finally, we are able to explain the trend of static dielectric constants followed by the three amides in terms of properties obtained from the simulations, namely hydrogen bond patterns and reorientational lifetimes.

Ab initio Car-Parrinello molecular dynamics simulations have been performed in order to investigate the solvation properties of Mg(2+) and Ca(2+) in fully deuterated methanol solution to better understand polarization effects induced by the ions. Charge transfer and dipole moment calculations have been performed to give more detailed insight on the role of the electronic reorganization and its effect on the first solvation shell stability. The perturbation of the methanol H-bond network has been investigated.

The structure of the solvation shell of Na+ and K+ in fully deuterated liquid methanol has been studied by ab initio Car-Parrinello molecular dynamics simulations. The solvent cage has been found relatively stable and this property has been explained by means of charge transfer and electrostatic interactions as was previously done for Li+ in the same solvent. The differences with Li+ such as the increase of the coordination number going from Li+ to K+ and the reduced stability of the cage have been ascribed to the increase in the ionic radius.

A conclusive study on the SERS band of pyridine occurring at about 1025 cm −1 was performed by a density functional theory (DFT) approach, by considering the ligand molecules bound to silver adclusters. The existence of (Ag 3 ) +2 surface active-sites, ascertained in Ag/SiO 2 colloids as metal adclusters stabilised by the interaction with the silica nanoparticles, was confirmed by DFT calculations, which satisfactorily account for the experimental findings.

A review of the recent theoretical and computational activity at the Chemistry Department of the University of Firenze in the field of molecular simulations of condensed phases is reported. The topics considered include quantitative methods for accurate free energy calculations, molecular dynamics of liquids and ionic solutions, chemical reactions in solutions, phase transformations and polymerization reactions at high pressures.

The adsorption of adenine on silver and gold surfaces has been investigated combining density functional theory calculations with surface-enhanced Raman scattering and angle-resolved X-ray photoelectron spectroscopy measurements, obtaining useful insight into the orientation and interaction of the nucleobase with the metal surfaces.

The reaction of ethylene in condensed phases under high pressure has been investigated by ab initio molecular dynamics. Both disordered and crystalline samples have been simulated, and some insights on the reaction mechanism have been obtained. System size effects have been investigated for the disordered samples. A polymerization reaction occurs by an ionic mechanism. In both the disordered and the crystal phases, the reaction products obtained (linear chains in the disordered systems and branched chains in the crystal) are in qualitative agreement with the experiments.

Wavelet transform has been used to correlate spectroscopic and structural properties from trajectories obtained by ab initio molecular dynamics simulations. This method has been applied to hydrogen bond dynamics of glycols in heavy water solutions, showing how the stretching frequency of the intramolecular O-H bond changes with the intermolecular hydrogen-bond distance. The resulting wavelet spectrograms have been interpreted according to H-bond strength and stability.